Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

We computationally study the Zika NS3 helicase, a biological motor, using ATP hydrolysis energy for nucleic acid remodeling. Through molecular mechanics and hybrid quantum mechanics/molecular mechanics simulations, we explore the conformational landscape of motif V, a conserved loop connecting the active sites for ATP hydrolysis and nucleic acid binding. ATP hydrolysis, initiated by a meta-phosphate group formation, involves the nucleophilic attack of a water molecule activated by Glu286 proton abstraction. Motif V hydrogen bonds to this water via the Gly415 backbone NH group, assisting hydrolysis. Posthydrolysis, free energy is released when the inorganic phosphate moves away from the coordination shell of the magnesium ion, inducing a significant shift in the conformational landscape of motif V to establish a hydrogen bond between the Gly415 NH group and Glu285. According to our simulations, the Zika NS3 helicase acts as a ratchet biological motor with motif V transitions steered by Gly415’s γ-phosphate sensing in the ATPase site.

Table S1.Dihedral angles of Motif V in conformations A and B of Zika NS3h in the X-ray structure (PDB: 6S0J).In bold the values of the analyzed dihedral angles.

Dihedral angle
Conformation

Figure S1 .
Figure S1.QM region selected to study the ATP hydrolysis reaction.The atoms included in the QM region are located inside the grey area.

Figure S2 .
Figure S2.Configurational space of Motif V during reactants state classical simulations of Zika NS3h.Each panel corresponds to the probability distribution of pair of Ψi/ Φi+1 torsional angles (in °) from Ψ405/ Φ406 to Ψ416/ Φ417.Colourbar represents the number of samples in each bin.The three different conformations found for the Ψ414/ Φ415 pair are labelled as A, B and C.

Figure S3 .
Figure S3.ATP hydrolysis in ZIKv-NS3 helicase in conformation A of motif V. (a) DFTB3/MM free energy profile along the path-CV (s) for ATP hydrolysis up to the formation of ADP and dihydrogen phosphate.(b) Evolution of the CVs along the path-CV.CVs are defined in Figure 3 of the manuscript.

Figure S4 .
Figure S4.Base-assisted mechanism for ATP hydrolysis in ZIKV-NS3 helicase in conformation B of motif V. (a) B3LYPD3/6-31G*/MM free energy profile along the path-CV (s) for ATP hydrolysis up to the formation of ADP and dihydrogen phosphate.(b) Evolution of the CVs along the path-CV.(c) CVs employed to study the base-assisted reaction mechanism.(d) Structure of the ratelimiting step (TS2).Motif V is shown in orange colour.

Figure S5 .
Figure S5.ATP hydrolysis in ZIKV-NS3 helicase in conformation B of motif V. (a) DFT3B3/MM free energy profile along the path-CV (s) for ATP hydrolysis up to the formation of ADP and dihydrogen phosphate.(b) Evolution of the CVs along the path-CV.The used CVs are those presented in Figure S3.

Figure S6 .
Figure S6.Substrate-assisted mechanism for the ATP hydrolysis in ZIKV-NS3 helicase in conformation A of motif V. (a) B3LYPD3/6-31G*/MM free energy profile along the path-CV (s) for ATP hydrolysis up to the formation of ADP and dihydrogen phosphate (b) Evolution of the CVs along the path-CV (c) CVs employed to study the substrate-assisted reaction mechanism.(d) Structure of the TS.Motif V is depicted in lime colour.

Figure S7 .
Figure S7.Proton tautomerism for ATP-hydrolysis products in ZIKV-NS3 helicase.(a) B3LYPD3/6-31G*/MM free energy profile along the path-CV (s) for the interconversion of P1, P2 and P3.(b) Evolution of the CVs along the path-CV.(c) CVs employed to study the double proton transfer from P1 to P2 and from this to P3.(d) Structure of P1, corresponding to ADP 3-and H2PO4 - coordinated to the Mg 2+ ion through a hydroxyl oxygen atom.(e) Structure of P2, corresponding to ADP 2-and HPO4 2-coordinated to the Mg 2+ .(f) Structure of P2, corresponding to ADP 3-and H2PO4 2-coordinated to the Mg 2+ ion through a non protonated oxygen atom.

Figure S8 .
Figure S8.Evolution of the full set of Collective variables (CVs) employed to study the detachment of inorganic phosphate followed by a conformational change in Motif V. (a) Evolution of the distance CVs along the path-CV.(b) Evolution of the angle and dihedral CVs along the path-CV.(c) Representation of the CVs employed to study the process.